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X-ray structure of human glutamate carboxypeptidase II (GCPII), the E424M inactive mutant, in complex with a inhibitor CFBzOG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% (v/v) pentaerythritol propoxylate PO/OH 5/4,
2 % (w/v) PEG 3350, and
100 mM Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.32 62.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.467 α = 90 b = 130.461 β = 90 c = 159.574 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.48 49.25 98.9 0.04 0.018 1 17.6 5.2 173724
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.5 93.9 0.673 0.314 0.849 1.9 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BI1 1.48 49.25 170339 3382 98.78 0.15708 0.15678 0.164 0.17197 0.1789 RANDOM 38.483
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.9 -2.37 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.459 r_dihedral_angle_4_deg 14.364 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_1_deg 5.884 r_long_range_B_refined 4.567 r_long_range_B_other 4.435 r_scangle_other 3.295 r_scbond_it 2.13 r_scbond_other 2.13 r_mcangle_other 2.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.459 r_dihedral_angle_4_deg 14.364 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_1_deg 5.884 r_long_range_B_refined 4.567 r_long_range_B_other 4.435 r_scangle_other 3.295 r_scbond_it 2.13 r_scbond_other 2.13 r_mcangle_other 2.041 r_mcangle_it 2.04 r_angle_other_deg 1.714 r_angle_refined_deg 1.691 r_mcbond_it 1.389 r_mcbond_other 1.386 r_chiral_restr 0.116 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5512 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement Aimless data scaling REFMAC phasing Coot model building XDS data reduction